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Gene Symbol Gene Name Start Stop Non-Synonymous Polymorphism

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Non-Synonymous Gene Symbol Gene Name Start Stop Polymorphism Sdcbp2 Syndecan binding protein (syntenin) 2 141,891,232 141,919,905 I82V Snph Syntaphilin 141,921,547 141,961,697 A411T, 415_420* Rad21l1 RAD21-like 1 (S. pombe) 141,984,729 142,009,665 LOC100363280 mCG140681-like 142,022,959 142,030,458 RGD1564048 Similar to Protein C20orf46 142,043961 142,047,717 Similar to Proteasome inhibitor PI31 LOC689852 142,058,695 142,083,908 subunit LOC100363380 Hypothetical LOC100363380 142,139,020 142,143,826 Rspo4 R-spondin family, member 4 142,185,028 142,216,015 Angpt4 Angiopoietin 4 142,249,115 142,282,307 Family with sequence similarity 110, Fam110a 142,326,013 142,328,572 member A LOC689884 Hypothetical protein LOC689884 142,335,923 142,336,396 LOC100363434 Ribosomal protein S29-like 142,339,596 142,341,169 RGD1304644 Similar to RIKEN cDNA 2310046K01 142,360,661 142,365,285 Scratch homolog 2, zinc finger protein Scrt2 142,434,272 142,445,984 (Drosophila) Srxn1 Sulfiredoxin 1 homolog (S. cerevisiae) 142,457,352 142,462,725 Tcf15 Transcription factor 15 142,491,664 142,497,446 Csnk2a1 Casein kinase 2, alpha 1 polypeptide 142,564,754 142,609,311 Tbc1d20 TBC1 domain family, member 20 142,623,713 142,640,197 RanBP-type and C3HC4-type zinc finger Rbck1 142,644,156 142,660,799 containing 1 Trib3 Tribbles homolog 3 (Drosophila) 142,664,641 142,670,135 Nrsn2 Neurensin 2 142,692,988 142,702,131 Sox12 SRY (sex determining region Y)-box 12 142,714,836 142,715,855 Zcchc3 Zinc finger, CCHC domain containing 3 142,727,648 142,730,465 LOC502684 Hypothetical protein LOC502684 142,745,094 142,764,314 Defb23 Defensin beta 23 142,780,126 142,784,338 Defb20 Defensin beta 20 142,804,804 142,807,427 Defb22 Defensin beta 22 142,813,671 142,817,950 Defb26 Defensin beta 26 142,834,066 142,837,469 Defb28 Defensin beta 28 142,838,348 142,853,944 LOC690064 Similar to 40S ribosomal protein S10 142,853,462 142,853,996 Defb29 Defensin beta 29 142,860,674 142,865,955 Defb19 Defensin beta 19 142,903,282 142,905,194 Defb21 Defensin beta 21 142,910,151 142,911,465 Defb24 Defensin beta 24 142,913,877 142,920,010 Defb27 Defensin beta 27 142,932,437 142,937,373 Defb36 Defensin beta 36 142,964,483 142,959,997 Defb25 Defensin beta 25 142,972,019 142,972,859 Rem1 RAS-like GTP binding 1 142,976,928 142,985,368 H13 Histocompatability 13 143,020,612 143,056,203 Mcts2 Malignant T cell amplified sequence 2 143,038,079 143,039,285 Id1 Inhibitor of DNA binding 1 143,086,162 143,087,289 LOC499921 Similar to high mobility group protein 1 143,095,429 143,096,094 Cox4i2 Cytochrome c oxidase subunit IV isoform 2 143,103,348 143,114,236 Bcl2l1 Bcl2-like1 143,129,087 143,180,199 LOC100363271 Ribosomal protein S2-like 143,149,520 143,150,401 Tpx2 TPX2, microtubule-associated, homolog 143,194,067 143,236,185 (Xenopus laevis) Mylk2 Myosin light chain kinase 2 143,252,183 143,263,849 Foxs1 Forkhead box S1 143,272,507 143,273,776 Dusp15 Dual specificity phosphatase 15 143,285,894 143,294,571 Tubulin tyrosine ligase-like family, Ttll9 143,304,937 143,351,359 member 9 Pdrg1 p53 and DNA damage regulated 1 143,353,054 143,359,223 XK, Kell blood group complex subunit- Xkr7 143,376,730 143,400,522 related family, member 7 RGD1305202 Similar to Protein C20orf160 143,409,027 143,423,744 Hck Hemopoietic cell kinase 143,447,697 143,490,281 Transmembrane 9 superfamily protein Tm9sf4 143,502,896 143,557,285 member 4 Tspyl3 TSPY-like 3 143,574,208 143,576,284 Plagl2 Pleiomorphic adenoma gene-like 2 143,578,877 143,592,055 Pofut1 Protein O-fucosyltransferase 1 143,592,269 143,614,466 LOC690246 Similar to 60S ribosomal protein L27a 143,631,638 143,632,082 LOC366233 Similar to 60S ribosomal protein L21 143,636,966 143,637,446 Kif3b Kinesin family member 3B 143,642,175 143,681,902 LOC690274 Hypothetical protein LOC690274 143,695,573 143,700,082 RGD1561878 Similar to mKIAA0978 protein 143,703,295 143,767,523 Similar to RIKEN cDNA 8430427H17 RGD1563510 143,774,195 143,904,844 gene Commd7 COMM domain containing 7 143,997,788 144,012,407 DNA (cytosine-5-)-methyltransferase 3 Dnmt3b 144,030,737 144,069,265 beta LOC690309 Similar to DNA methyltransferase 3B 144,080,177 144,112,035 Similar to Alpha-enolase (2-phospho-D- LOC689804 glycerate hydro-lyase) (Non-neural 144,109,924 144,111,554 enolase) (Enolase 1) Microtubule-associated protein, RP/EB Mapre1 144,120,532 144,148,856 family member 1 RGD1560257 Similar to hypothetical protein A630008I04 144,161,795 144,225,579 Efcab8 EF-hand calcium binding domain 8 144,163,986 144,169,818 Spag4l Sperm associated antigen 4-like 144,236,963 144,257,526 S10L Bactericidal/permeability-increasing Bpil1 144,260,247 144,279,234 protein-like 1 Bactericidal/permeability-increasing Bpil3 144,293,297 144,297,498 protein-like 3 Rya3 Antimicrobial peptide RYA3 144,303,258 144,317,875 RY2G5 Potential ligand-binding protein 144,325,761 144,350,230 LOC100359775 Splunc6-like 144,367,912 144,380,189 Psp Parotid secretory protein 144,395,541 144,403,499 Smgb Neonatal submandibular gland protein B 144,423,417 144,435,625 Similar to Short palate, lung and nasal LOC690402 epithelium carcinoma-associated protein 3 144,511,823 144,521,745 homolog precursor Palate, lung, and nasal epithelium Plunc 144,529,855 144,535,598 associated Similar to NIMA (never in mitosis gene a)- LOC690426 144,536,781 144,546,511 related kinase 2 Similar to Palate lung and nasal carcinoma- RGD1559748 144,548,148 144,554,452 like protein precursor Similar to von Ebner minor salivary gland RGD1563047 144,601,201 144,635,308 M352T protein LOC690479 Hypothetical protein LOC690479 144,638,920 144,652,523 E196D, N205S, P308L, I319M LOC690486 Similar to 60S ribosomal protein L7 144,659,980 144,660,754 D196E, S205N, LOC690497 Similar to MORF-related gene X 144,712,002 144,712,695 L308P, M319I LOC690507 Similar to Vomeromodulin 144,723,203 144,733,928 Similar to HMG-1 (High mobility group LOC690521 144,762,561 144,763,202 protein B1) CDK5 regulatory subunit associated Cdk5rap1 144,803,213 144,840,056 protein 1 Snta1 Syntrophin, acidic 1 144,843,678 144,874,238 Core-binding factor, runt domain, alpha Cbfa2t2 144,904,533 145,007,851 subunit 2; translocated to, 2 LOC690027 Similar to spermine synthase 144,911,210 144,912,792 LOC683008 Similar to spermine synthase 144,911,661 144,912,847 LOC100360105 Zinc finger, FYVE domain containing 21 144,981,179 144,999,578 N-terminal EF-hand calcium binding Necab3 145,017,420 145,031,905 162_163** protein 3 Similar to chromosome 20 open reading RGD1561517 145,022,077 145,023,268 frame 144 E2f1 E2F transcription factor 1 145,032,489 145,043,729 Pxmp4 Peroxisomal membrane protein 4 145,061,123 145,078,370 LOC296300 Similar to zinc finger protein 341 145,086,839 145,105,846 Eukaryotic translation elongation factor 1 LOC100360150 145,106,442 145,114,354 alpha 2 Zfp341 Zinc finger protein 341 145,108,413 145,124,023 LOC100359642 rCG37275-like 145,138,905 145,176,471 Chmp4b Chromatin modifying protein 4B 145,178,263 145,179,851 LOC690589 Similar to 60S ribosomal protein L7a 145,187,694 145,204,782 LOC690597 Similar to 60S ribosomal protein L38 145,254,907 145,255,116 Raly RNA binding protein, autoantigenic 145,275,832 145,337,808 LOC100360250 Hypothetical LOC100360250 145,327,005 145,327,215 Eukaryotic translation initiation factor 2, Eif2s2 145,346,392 145,367,117 subunit 2 beta Asip Agouti signaling protein 145,445,175 145,536,831 36_44* LOC100360304 Hypothetical LOC100360304 145,467,378 145,467,743 Ahcy Adenosylhomocysteinase 145,544,834 145,560,058 LOC366235 Similar to 60S ribosomal protein L12 145,587,354 145,587,927 LOC690622 Hypothetical protein LOC690622 145,621,455 145,622,913 Itchy E3 ubiquitin protein ligase homolog Itch 145,644,315 145,707,190 (mouse) Dynlrb1 Dynein light chain roadblock-type 1 145,718,890 145,740,187 Microtubule-associated protein 1 light Map1lc3a 145,758,939 145,760,532 chain 3 alpha Phosphatidylinositol glycan anchor Pigu 145,760,693 145,841,916 biosynthesis, class U Tumor protein p53 inducible nuclear Tp53inp2 145,878,005 145,886,088 protein 2 Ncoa6 Nuclear receptor coactivator 6 145,886,874 145,957,928 258_263* Ggt7 Gamma-glutamyltransferase 7 145,987,531 146,010,922 Acyl-CoA synthetase short-chain family Acss2 146,013,995 146,057,119 member 2 Gss Glutathione synthetase 146,057,517 146,087,820 K16E Myosin, heavy chain 7B, cardiac muscle, Myh7b 146,115,687 146,139,441 beta Transient receptor potential cation channel, Trpc4ap 146,139,493 146,206,625 Y166C subfamily C, member 4 associated protein Similar to Glyceraldehyde-3-phosphate LOC690264 146,189,074 146,190,106 dehydrogenase ER degradation enhancer, mannosidase Edem2 146,215,243 146,241,062 alpha-like 2 Procr Protein C receptor, endothelial 146,268,567 146,273,718 LOC100360401 Hypothetical LOC100360401 146,284,682 146,285,087 Cep250 Centrosomal protein 250kDa 146,378,670 146,407,642 M387V LOC100359643 mCG58586-like 146,411,621 146,412,464 Ergic3 ERGIC and golgi 3 146,416,599 146,426,325 Fer1l4 Fer-1-like 4 (C.
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    ARTICLE DOI: 10.1038/s41467-018-04864-8 OPEN Targeting EZH2 reactivates a breast cancer subtype-specific anti-metastatic transcriptional program Alison Hirukawa1,2, Harvey W. Smith1, Dongmei Zuo1, Catherine R. Dufour1, Paul Savage 1, Nicholas Bertos 1, Radia M. Johnson1, Tung Bui1,2, Guillaume Bourque3,4, Mark Basik5,6, Vincent Giguère 1,2,6, Morag Park1,2,6 & William J. Muller1,2,6 1234567890():,; Emerging evidence has illustrated the importance of epigenomic reprogramming in cancer, with altered post-translational modifications of histones contributing to pathogenesis. However, the contributions of histone modifiers to breast cancer progression are unclear, and how these processes vary between molecular subtypes has yet to be adequately addressed. Here we report that genetic or pharmacological targeting of the epigenetic modifier Ezh2 dramatically hinders metastatic behaviour in both a mouse model of breast cancer and patient-derived xenografts reflective of the Luminal B subtype. We further define a subtype- specific molecular mechanism whereby EZH2 maintains H3K27me3-mediated repression of the FOXC1 gene, thereby inactivating a FOXC1-driven, anti-invasive transcriptional program. We demonstrate that higher FOXC1 is predictive of favourable outcome specifically in Luminal B breast cancer patients and establish the use of EZH2 methyltransferase inhibitors as a viable strategy to block metastasis in Luminal B breast cancer, where options for targeted therapy are limited. 1 Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada. 2 Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada. 3 McGill University, Génome Québec Innovation Centre, Montréal, QC H3A 0G1, Canada. 4 Department of Human Genetics, McGill University, Montréal, QC H3A 1A3, Canada.
  • Ingenuity Pathway Analysis of Differentially Expressed Genes Involved in Signaling Pathways and Molecular Networks in Rhoe Gene‑Edited Cardiomyocytes

    Ingenuity Pathway Analysis of Differentially Expressed Genes Involved in Signaling Pathways and Molecular Networks in Rhoe Gene‑Edited Cardiomyocytes

    INTERNATIONAL JOURNAL OF MOleCular meDICine 46: 1225-1238, 2020 Ingenuity pathway analysis of differentially expressed genes involved in signaling pathways and molecular networks in RhoE gene‑edited cardiomyocytes ZHONGMING SHAO1*, KEKE WANG1*, SHUYA ZHANG2, JIANLING YUAN1, XIAOMING LIAO1, CAIXIA WU1, YUAN ZOU1, YANPING HA1, ZHIHUA SHEN1, JUNLI GUO2 and WEI JIE1,2 1Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, Guangdong 524023; 2Hainan Provincial Key Laboratory for Tropical Cardiovascular Diseases Research and Key Laboratory of Emergency and Trauma of Ministry of Education, Institute of Cardiovascular Research of The First Affiliated Hospital, Hainan Medical University, Haikou, Hainan 571199, P.R. China Received January 7, 2020; Accepted May 20, 2020 DOI: 10.3892/ijmm.2020.4661 Abstract. RhoE/Rnd3 is an atypical member of the Rho super- injury and abnormalities, cell‑to‑cell signaling and interaction, family of proteins, However, the global biological function and molecular transport. In addition, 885 upstream regulators profile of this protein remains unsolved. In the present study, a were enriched, including 59 molecules that were predicated RhoE‑knockout H9C2 cardiomyocyte cell line was established to be strongly activated (Z‑score >2) and 60 molecules that using CRISPR/Cas9 technology, following which differentially were predicated to be significantly inhibited (Z‑scores <‑2). In expressed genes (DEGs) between the knockout and wild‑type particular, 33 regulatory effects and 25 networks were revealed cell lines were screened using whole genome expression gene to be associated with the DEGs. Among them, the most signifi- chips. A total of 829 DEGs, including 417 upregulated and cant regulatory effects were ‘adhesion of endothelial cells’ and 412 downregulated, were identified using the threshold of ‘recruitment of myeloid cells’ and the top network was ‘neuro- fold changes ≥1.2 and P<0.05.